{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Mark Sterken"],"organism":["Globodera pallida"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16117"],"description":["We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Transcriptome sequencing was performed by BGI Hong Kong. Two samples (B_4.2_1,5; B_4.3_1,5) were not taken along for sequencing because of a failed library prep."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - For RNA sequencing stranded libraries were sequenced on the DNBseq platform, generating on an average of 104 million 150 bp clean reads per sample.","Nucleic Acid Extraction - Total RNA was extracted with the Maxwell 16 LEV-plant RNA kit (Promega, USA), according to the manufacturer’s instructions.","Sample Collection - In vitro infection assays were performed as described by Goverse et al. (2000) with additions made by Zheng et al. (2022) and Schaveling et al., (2025). In brief, we used cuttings of the susceptible potato cultivar Desirée, which were grown on Gamborg B5 medium supplemented with either 20 g/L or 1.5 g/L of sucrose. After 14 days, cuttings were inoculated with 100 G. pallida Rookmaker J2s per plate.  We harvested infected roots at 1, 3, 6, and 9 days post inoculation (dpi). At 1 and 3 dpi, infected root segments of 15 plants were pooled per sample and at 6 and 9 dpi, infected root segments of 10 plants were pooled per sample.","Library Construction - RNA samples were send for mRNA sequencing to BGI Genomics (Hong Kong, China). 1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers; 4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Perform PCR amplification; 7. Library quality control; 8. Library circularization; 9. The library was amplified to make DNA nanoball (DNB); 10. Sequencing on DNBSEQ (DNBSEQ Technology) platform."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Reads were mapped against the G. pallida Rookmaker genome (PRJEB91928) using hisat2. The resulting BAM files were loaded into SeqMonk for analysis and TPM values were generated."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-G400","Maxwell 16 LEV-plant RNA kit"],"study_type":["RNA-seq of coding RNA"],"species":["Globodera pallida"],"pubmed_authors":["Stefan van de Ruitenbeek","Arno Schaveling","Mark Sterken","Geert Smant"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome sequencing on a time series of potato infected with Globodera pallida to explore the sex determination","description":"We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Transcriptome sequencing was performed by BGI Hong Kong. Two samples (B_4.2_1,5; B_4.3_1,5) were not taken along for sequencing because of a failed library prep.","dates":{"release":"2025-11-25T00:00:00Z","modification":"2026-05-30T17:05:20.257Z","creation":"2025-11-14T11:39:32.508Z"},"accession":"E-MTAB-16117","cross_references":{"ENA":["ERP184430"],"Biostudies":["E-MTAB-15069"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}